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Encapsulin Nanocompartments for Biomanufacturing Applications

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Part of the Microbiology Monographs book series (MICROMONO,volume 37)

Abstract

Enzyme scaffolding is an emerging technique for enhancing yield and efficiency of biomanufacturing processes for generating high-value products. Of the many scaffolds available for in vivo and cell-free applications, encapsulin protein nanocompartments have garnered recent attention due to their desirable properties as a scaffold, such as robust self-assembly, high thermal stability, and the inherent ability to package and display enzymatic cargo. In this chapter, we discuss basic and advanced methods for encapsulin engineering, as well as the many encapsulin-based biomanufacturing systems that have been built. We subsequently discuss how these advances can be applied to increasingly complex encapsulin systems and look to the future of biomanufacturing in tunable protein nanocompartments.

Keywords

  • Capsids
  • Synthetic biology
  • Protein self-assembly
  • Scaffolds
  • Enzyme cascades

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References

  • Adamson LSR, Tasneem N, Andreas MP, Close W, Jenner EN, Szyszka TN, Young R, Cheah LC, Norman A, Mac Dermott-Opeskin HI, O’Mara ML, Sainsbury F, Giessen TW, Lau YH (2022) Pore structure controls stability and molecular flux in engineered protein cages. Sci Adv 8(5):eabl7346. https://doi.org/10.1126/sciadv.abl7346

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  • Akita F et al (2007) The crystal structure of a virus-like particle from the hyperthermophilic archaeon Pyrococcus furiosus provides insight into the evolution of viruses. J Mol Biol 368:1469–1483

    CAS  PubMed  CrossRef  Google Scholar 

  • Altenburg WJ, Rollins N, Silver PA, Giessen TW (2021) Exploring targeting peptide-shell interactions in encapsulin nanocompartments. Sci Rep 11:1–9

    CrossRef  CAS  Google Scholar 

  • Andreas MP, Giessen TW (2021) Large-scale computational discovery and analysis of virus-derived microbial nanocompartments. Nat Commun 12:4748

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Bae Y et al (2018) Engineering tunable dual functional protein cage nanoparticles using bacterial superglue. Biomacromolecules 19:2896–2904

    CAS  PubMed  CrossRef  Google Scholar 

  • Bamford DH, Grimes JM, Stuart DI (2005) What does structure tell us about virus evolution? Curr Opin Struct Biol 15:655–663

    CAS  PubMed  CrossRef  Google Scholar 

  • Banaszynski LA, Liu CW, Wandless TJ (2005) Characterization of the FKBP. Rapamycin.FRB ternary complex. J Am Chem Soc 127:4715–4721

    CAS  PubMed  CrossRef  Google Scholar 

  • Borden JS, Savage DF (2021) New discoveries expand possibilities for carboxysome engineering. Curr Opin Microbiol 61:58–66

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Caspar DLD, Klug A (1962) Physical principles in the construction of regular viruses. In: Cold Spring Harbor symposia on quantitative biology, vol 27. Cold Spring Harbor Laboratory Press, pp 1–24

    Google Scholar 

  • Cassidy-Amstutz C et al (2016) Identification of a minimal peptide tag for in vivo and in vitro loading of encapsulin. Biochemistry 55:3461–3468

    CAS  PubMed  CrossRef  Google Scholar 

  • Choi B et al (2016) Effective delivery of antigen–encapsulin nanoparticle fusions to dendritic cells leads to antigen-specific cytotoxic T cell activation and tumor rejection. ACS Nano 10:7339–7350

    CAS  PubMed  CrossRef  Google Scholar 

  • Choi H et al (2021) Load and display: engineering encapsulin as a modular nanoplatform for protein-cargo encapsulation and protein-ligand decoration using split intein and SpyTag/SpyCatcher. Biomacromolecules 22:3028–3039

    CAS  PubMed  CrossRef  Google Scholar 

  • Diaz D, Vidal X, Sunna A, Care A (2021) Bioengineering a light-responsive encapsulin nanoreactor: a potential tool for in vitro photodynamic therapy. ACS Appl Mater Interfaces 13:7977–7986

    CAS  PubMed  CrossRef  Google Scholar 

  • Giessen TW, Jones JA, Cristie-David AS, Andreas MP (2021) Triggered reversible disassembly of an engineered protein nanocage. Angew Chemie Int Ed. https://doi.org/10.1002/anie.202110318

  • Giessen TW, Silver PA (2017) Widespread distribution of encapsulin nanocompartments reveals functional diversity. Nat Microbiol 2:1–11

    CrossRef  Google Scholar 

  • Giessen TW et al (2019) Large protein organelles form a new iron sequestration system with high storage capacity. elife 8:e46070

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • Hall MP et al (2012) Engineered luciferase reporter from a deep sea shrimp utilizing a novel imidazopyrazinone substrate. ACS Chem Biol 7:1848–1857

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • He D et al (2016) Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments. elife 5:e18972

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • Helgstrand C et al (2003) The refined structure of a protein catenane: the HK97 bacteriophage capsid at 3.44 Å resolution. J Mol Biol 334:885–899

    CAS  PubMed  CrossRef  Google Scholar 

  • Jathoul AP et al (2015) Deep in vivo photoacoustic imaging of mammalian tissues using a tyrosinase-based genetic reporter. Nat Photonics 9:239–246

    CAS  CrossRef  Google Scholar 

  • Jenkins MC, Lutz S (2021) Encapsulin nanocontainers as versatile scaffolds for the development of artificial metabolons. ACS Synth Biol 10:857–869

    CAS  PubMed  CrossRef  Google Scholar 

  • Jones JA, Giessen TW (2021) Advances in encapsulin nanocompartment biology and engineering. Biotechnol Bioeng 118:491–505

    CAS  PubMed  CrossRef  Google Scholar 

  • Jordan PC et al (2016) Self-assembling biomolecular catalysts for hydrogen production. Nat Chem 8:179–185

    CAS  PubMed  CrossRef  Google Scholar 

  • Kawamoto S et al (2001) Molecular and functional analyses of the gene (eshA) encoding the 52-kilodalton protein of Streptomyces coelicolor A3 (2) required for antibiotic production. J Bacteriol 183:6009–6016

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Kelley L-LC et al (2007) Structure of the hypothetical protein PF0899 from Pyrococcus furiosus at 1.85 Å resolution. Acta Crystallogr Sect F 63:549

    CrossRef  CAS  Google Scholar 

  • Klem R, De Ruiter MV, Cornelissen JJLM (2018) Protecting encapsulin nanoparticles with cysteine-knot miniproteins. Mol Pharm 15:2991–2996

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Kodama Y, Hu C-D (2010) An improved bimolecular fluorescence complementation assay with a high signal-to-noise ratio. BioTechniques 49:793–805

    CAS  PubMed  CrossRef  Google Scholar 

  • Künzle M, Mangler J, Lach M, Beck T (2018) Peptide-directed encapsulation of inorganic nanoparticles into protein containers. Nanoscale 10:22917–22926

    PubMed  CrossRef  Google Scholar 

  • Kwak J, McCue LA, Trczianka K, Kendrick KE (2001) Identification and characterization of a developmentally regulated protein, EshA, required for sporogenic hyphal branches in Streptomyces griseus. J Bacteriol 183:3004–3015

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Lagoutte P et al (2018) Simultaneous surface display and cargo loading of encapsulin nanocompartments and their use for rational vaccine design. Vaccine 36:3622–3628

    CAS  PubMed  CrossRef  Google Scholar 

  • Lau YH, Giessen TW, Altenburg WJ, Silver PA (2018) Prokaryotic nanocompartments form synthetic organelles in a eukaryote. Nat Commun 9:1–7

    CrossRef  CAS  Google Scholar 

  • Lee S-Y, Lee J-H, Chang J-H, Lee J-H (2011) Inorganic nanomaterial-based biocatalysts. BMB Rep 44:77–86

    CAS  PubMed  CrossRef  Google Scholar 

  • Lee T, Carpenter TS, D’haeseleer P, Savage DF, Yung MC (2020) Encapsulin carrier proteins for enhanced expression of antimicrobial peptides. Biotechnol Bioeng 117:603–613

    CAS  PubMed  CrossRef  Google Scholar 

  • Liu A, Yang L, Traulsen C-H, Cornelissen J (2017) Immobilization of catalytic virus-like particles in a flow reactor. Chem Commun 53:7632–7634

    CAS  CrossRef  Google Scholar 

  • Lončar N, Rozeboom HJ, Franken LE, Stuart MCA, Fraaije MW (2020) Structure of a robust bacterial protein cage and its application as a versatile biocatalytic platform through enzyme encapsulation. Biochem Biophys Res Commun 529:548–553

    PubMed  CrossRef  CAS  Google Scholar 

  • London N, Raveh B, Cohen E, Fathi G, Schueler-Furman O (2011) Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions. Nucleic Acids Res 39:W249–W253

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Maynard-Smith LA, Chen L, Banaszynski LA, Ooi AGL, Wandless TJ (2007) A directed approach for engineering conditional protein stability using biologically silent small molecules. J Biol Chem 282:24866–24872

    CAS  PubMed  CrossRef  Google Scholar 

  • McHugh CA et al (2014) A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress. EMBO J 33:1896–1911

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Mironova KE et al (2013) Genetically encoded immunophotosensitizer 4D5scFv-miniSOG is a highly selective agent for targeted photokilling of tumor cells in vitro. Theranostics 3:831

    PubMed  PubMed Central  CrossRef  CAS  Google Scholar 

  • Moon H, Bae Y, Kim H, Kang S (2016) Plug-and-playable fluorescent cell imaging modular toolkits using the bacterial superglue, SpyTag/SpyCatcher. Chem Commun52:14051–14054

    CAS  CrossRef  Google Scholar 

  • Moon H, Lee J, Min J, Kang S (2014a) Developing genetically engineered encapsulin protein cage nanoparticles as a targeted delivery nanoplatform. Biomacromolecules 15:3794–3801

    CAS  PubMed  CrossRef  Google Scholar 

  • Moon H et al (2014b) Genetically engineering encapsulin protein cage nanoparticle as a SCC-7 cell targeting optical nanoprobe. Biomater Res 18:1–7

    CrossRef  Google Scholar 

  • Nichols RJ, Cassidy-Amstutz C, Chaijarasphong T, Savage DF (2017) Encapsulins: molecular biology of the shell. Crit Rev Biochem Mol Biol 52:583–594

    CAS  PubMed  CrossRef  Google Scholar 

  • Nichols RJ et al (2021) Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism. elife 10:e59288

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Putri RM, Fredy JW, Cornelissen JJLM, Koay MST, Katsonis N (2016) Labelling bacterial nanocages with photo-switchable fluorophores. ChemPhysChem 17:1815–1818

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Putri RM et al (2017) Structural characterization of native and modified encapsulins as nanoplatforms for in vitro catalysis and cellular uptake. ACS Nano 11:12796–12804

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Rahmanpour R, Bugg TDH (2013) Assembly in vitro of Rhodococcus jostii RHA 1 encapsulin and peroxidase DypB to form a nanocompartment. FEBS J 280:2097–2104

    CAS  PubMed  CrossRef  Google Scholar 

  • Raveh B, London N, Zimmerman L, Schueler-Furman O (2011) Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors. PLoS One 6:e18934

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Rurup WF, Cornelissen JJLM, Koay MST (2015) Recombinant expression and purification of “virus-like” bacterial encapsulin protein cages. In: Protein Cages. Springer, pp 61–67

    CrossRef  Google Scholar 

  • Rurup WF, Snijder J, Koay MST, Heck AJR, Cornelissen JJLM (2014) Self-sorting of foreign proteins in a bacterial nanocompartment. J Am Chem Soc 136:3828–3832

    CAS  PubMed  CrossRef  Google Scholar 

  • Saito N, Matsubara K, Watanabe M, Kato F, Ochi K (2003) Genetic and biochemical characterization of EshA, a protein that forms large multimers and affects developmental processes in Streptomyces griseus. J Biol Chem 278:5902–5911

    CAS  PubMed  CrossRef  Google Scholar 

  • Salvachua D, Prieto A, Martinez AT, Martinez MJ (2013) Characterization of a novel dye-decolorizing peroxidase (DyP)-type enzyme from Irpex lacteus and its application in enzymatic hydrolysis of wheat straw. Appl Environ Microbiol 79:4316–4324

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Sassolas A, Blum LJ, Leca-Bouvier BD (2012) Immobilization strategies to develop enzymatic biosensors. Biotechnol Adv 30:489–511

    CAS  PubMed  CrossRef  Google Scholar 

  • Shah NH, Muir TW (2014) Inteins: nature’s gift to protein chemists. Chem Sci 5:446–461

    CAS  PubMed  CrossRef  Google Scholar 

  • Sheldon RA, Basso A, Brady D (2021) New frontiers in enzyme immobilisation: robust biocatalysts for a circular bio-based economy. Chem Soc Rev 50(10):5850–5862

    CAS  PubMed  CrossRef  Google Scholar 

  • Sheldon RA, van Pelt S (2013) Enzyme immobilisation in biocatalysis: why, what and how. Chem Soc Rev 42:6223–6235

    CAS  PubMed  CrossRef  Google Scholar 

  • Sigmund F et al (2018) Bacterial encapsulins as orthogonal compartments for mammalian cell engineering. Nat Commun 9:1–14

    CAS  CrossRef  Google Scholar 

  • Sonotaki S et al (2017) Successful PEGylation of hollow encapsulin nanoparticles from Rhodococcus erythropolis N771 without affecting their disassembly and reassembly properties. Biomater Sci 5:1082–1089

    CAS  PubMed  CrossRef  Google Scholar 

  • Stritzker J et al (2013) Vaccinia virus-mediated melanin production allows MR and optoacoustic deep tissue imaging and laser-induced thermotherapy of cancer. Proc Natl Acad Sci 110:3316–3320

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Sutter M et al (2008) Structural basis of enzyme encapsulation into a bacterial nanocompartment. Nat Struct Mol Biol 15:939–947

    CAS  PubMed  CrossRef  Google Scholar 

  • Szyszka TN, Jenner EN, Tasneem N, Lau YH (2021) Molecular display on protein nanocompartments: design strategies and systems applications. Chem Syst Chem 4:2

    Google Scholar 

  • Tamura A et al (2015) Packaging guest proteins into the encapsulin nanocompartment from Rhodococcus erythropolis N771. Biotechnol Bioeng 112:13–20

    CAS  PubMed  CrossRef  Google Scholar 

  • Triccas JA et al (1996) A 35-kilodalton protein is a major target of the human immune response to mycobacterium leprae. Infect Immun 64:5171–5177

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

  • Valdés-Stauber N, Scherer S (1994) Isolation and characterization of Linocin M18, a bacteriocin produced by Brevibacterium linens. Appl Environ Microbiol 60:3809–3814

    PubMed  PubMed Central  CrossRef  Google Scholar 

  • Wikoff WR et al (2000) Topologically linked protein rings in the bacteriophage HK97 capsid. Science 289:2129–2133

    CAS  PubMed  CrossRef  Google Scholar 

  • Williams EM, Jung SM, Coffman JL, Lutz S (2018) Pore engineering for enhanced mass transport in encapsulin nanocompartments. ACS Synth Biol 7:2514–2517

    CAS  PubMed  CrossRef  Google Scholar 

  • Winter N et al (1995) Characterization of the gene encoding the immunodominant 35 kDa protein of mycobacterium leprae. Mol Microbiol 16:865–876

    CAS  PubMed  CrossRef  Google Scholar 

  • Zakeri B et al (2012) Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. Proc Natl Acad Sci 109:E690–E697

    CAS  PubMed  PubMed Central  CrossRef  Google Scholar 

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Acknowledgements

YHL acknowledges funding from the Australian Research Council (DE190100624) and the Westpac Scholars Trust (WRF2020). LSRA acknowledges funding from a CSIRO SynBio Future Science Platform top-up scholarship.

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Correspondence to Yu Heng Lau .

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Szyszka, T.N., Adamson, L.S.R., Lau, Y.H. (2022). Encapsulin Nanocompartments for Biomanufacturing Applications. In: Rehm, B.H.A., Wibowo, D. (eds) Microbial Production of High-Value Products. Microbiology Monographs, vol 37. Springer, Cham. https://doi.org/10.1007/978-3-031-06600-9_12

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